Characterizing the microbiome of farmed Pacific oysters from British Columbia and Alaska

Pacific oyster (Crassostrea gigas) aquaculture is one of the largest suppliers of seafood worldwide. For instance, oyster production from British Columbia contributes 60% of the annual shellfish production in Canada. With the expanding industry, there have been growing incidents of mortality events in hatchery production, causing the seed stock shortages limiting sales to nursery growers. Recent studies have attempted to characterize the microbiome (pathobiome) associated with mortality; however, differing effects of harvest sites, tissues, age, and abiotic stresses on the oyster microbiome make it challenging to identify the mortality causes. Thus, there is a need to define the core members of oyster microbiome to serve as a baseline for future hypotheses testing. In the current study, Pacific oysters were obtained from two farm sites differing in location, sampling time, and production stages with the goal of identifying microbial taxa that are consistently found in C. gigas. Bacteria in the genus Sulfitobacter and phylum Planctomycetes, which are known to oxidize sulfur and fix nitrogen, respectively, were identified in all samples. To determine taxa only associated with mortality events, the microbiome of post-metamorphosis hatchery oysters (spat) that had experienced mortality were compared to spat that had not. Bacteria in the order Alteromonadales and genus Roseovarius were associated with spat sampled before, during and after peak mortality. No significant (Kruskal Wallis pair-wise; p>0.05) differences in microbiome composition and diversity were observed between populations that experienced or did not experience mortality. Irrespective of mortality events, however, the composition and relative abundance of microbial taxa changed as the oysters aged, with the highest dissimilarity in microbial composition and diversity occurring among the youngest spat. High dissimilarity in the microbiome of the youngest spat may reflect; i) diseased states of developing spat, some of which experienced mortality while others showed a stochastic microbiome pattern and, ii) a “maturing” microbiome after metamorphosis in rapidly developing spat. The common taxa identified in the oyster samples examined in this study are linked to important biogeochemical cycles and may be part of a core microbiome related to the filter-feeding behaviour of oysters and the surrounding environment.Science, Faculty ofMicrobiology and Immunology, Department ofGraduat